how to order paired-end reads to use in kaiju?
I am trying to use kaiju for a taxonomic analysis and when trying to use the .fastq files resulting from the process with Trimmomatic, I get an error because the sequences of reads are not in the same order in files_1.fastq and files_2.fastq (as described on github for kaiju is a requirement). Could someone guide me on how to deal with this situation?
Thank you very much in advance
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